Support mixed Argos and Facets Annotate maf files in main workflow

mskcc / pluto-cwl

CWL workflows for helix filter scripts

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Support mixed Argos and Facets Annotate maf files in main workflow #6

Closed stevekm closed 4 years ago

stevekm commented 4 years ago

Right now, the main workflow.cwl can take either Argos .muts.maf files or Facets Suite annotated .maf files as input in the mutation_maf_files fields, but it will likely break if a mix of the two files is used

This should be easy to fix if we just swap concat.cwl usage in the analysis and portal workflows with concat-tables.cwl which can fill in missing columns. Make sure to use NA for NA values.

stevekm commented 4 years ago

this might be complicated by the presence of comments in the maf files, which the concat-tables.py script does not currently handle

stevekm commented 4 years ago

this is implemented now